·Adenovirus genomes can be generated from enrichment bait sets containing just 14 references.·Highly specific enrichment can be observed in a variety of sample matrices including stool.·Adenovirus ...enrichment success is not influenced by type even for types not covered in the bait set.
Background: Human Adenoviruses are a common cause of disease and can cause significant morbidity and mortality in immunocompromised patients. Nosocomial transmission events can occur with whole genome sequencing playing a crucial role. This study evaluates the performance of a custom designed SureSelectXT target enrichment assay based on 14 adenovirus genomes for sequencing direct from clinical samples.
Methods: Modifications were made to the SureSelectXT low input protocol to enhance performance for viral targets. Consensus sequences were generated using an in-house designed three stage bioinformatics pipeline. We assessed, percentage of on target reads, average depth of coverage and percentage genome coverage to determine assay performance across a range of sample matrices.
Results: Whole genome sequences were successfully generated for 91.6 % of samples assessed. Adenovirus DNA concentration was a good indicator of enrichment success. Highly specific enrichment was observed with only 6 % of samples showing < 50 % on target reads. Respiratory and faecal samples performed well where bloods showed higher levels of non-specific enrichment likely confounded by low adenovirus DNA concentrations. Protocol performance did not appear impacted by Adenovirus type or species.
Conclusion: Overall performance of this modified SureSelectXT protocol appears in line with previously published works although there are some confounding factors requiring further investigation. The use of a small RNA bait set has the potential to reduce associated costs which can be prohibitive.
The increased adoption of genomic strategies in the clinic makes it imperative for diagnostic laboratories to improve the efficiency of variant interpretation. Clinical exome sequencing (CES) is ...becoming a valuable diagnostic tool, capable of meeting the diagnostic demand imposed by the vast array of different rare monogenic disorders. We have assessed a clinician-led and phenotype-based approach for virtual gene panel generation for analysis of targeted CES in patients with rare disease in a single institution.
Retrospective survey of 400 consecutive cases presumed by clinicians to have rare monogenic disorders, referred on singleton basis for targeted CES. We evaluated diagnostic yield and variant workload to characterise the usefulness of a clinician-led approach for generation of virtual gene panels that can incorporate up to three different phenotype-driven gene selection methods.
Abnormalities of the nervous system (54.5%), including intellectual disability, head and neck (19%), skeletal system (16%), ear (15%) and eye (15%) were the most common clinical features reported in referrals. Combined phenotype-driven strategies for virtual gene panel generation were used in 57% of cases. On average, 7.3 variants (median=5) per case were retained for clinical interpretation. The overall diagnostic rate of proband-only CES using personalised phenotype-driven virtual gene panels was 24%.
Our results show that personalised virtual gene panels are a cost-effective approach for variant analysis of CES, maintaining diagnostic yield and optimising the use of resources for clinical genomic sequencing in the clinic.
EGFR mutation testing of tumor samples is routinely performed to predict sensitivity to treatment with tyrosine kinase inhibitors for patients with non-small cell lung cancer. At least 9 different ...methodologies are employed in UK laboratories, and the aim of this study was to compare the sensitivity of different methods for the detection of EGFR mutations. Participating laboratories were sent coded samples with varying mutation loads (from 0% to 15%) to be tested for the p.Leu858Arg (p.L858R) missense mutation and c.2235_2249del exon 19 deletion. The p.L858R mutation and deletions within exon 19 of the EGFR gene account for ∼90% of mutation-positive cases. The 11 laboratories used their standard testing method(s) and submitted 15 sets of results for the p.L858R samples and 10 for the exon 19 deletion. The p.Leu858Arg (p.L858R) mutation was detected at levels between 1% and 7.5% by Sanger sequencing, pyrosequencing, real-time polymerase chain reaction (PCR), amplification refractory mutation system, and capillary electrophoresis single-strand conformation analysis. The c.2235_2249del mutation was detected at 1% to 5% by fragment size analysis, Sanger sequencing or real-time PCR. A mutation was detected in 24/25 (96%) of the samples tested which contained 5% mutated DNA. The 1% sensitivity claimed for commercial real-time PCR-targeted EGFR tests was achieved and our results show greater sensitivity for the Sanger sequencing and pyrosequencing screening methods compared to the 10% to 20% detection levels cited on clinical diagnostic reports. We conclude that multiple methodologies are suitable for the detection of acquired EGFR mutations.
This qualitative study investigated the leadership strategies superintendents implemented in response to changes in school district budget development that have taken place since the Chapter 97 (PART ...A) of the New York State Laws of 2011 became a general municipal and education law. The study explored the relationship between the Real Property Tax Cap legislation and budget development in school districts where the budget put to voters exceeded the maximum allowable tax levy limit. The lens for investigating the impact of Real Property Tax Cap legislation was perceptions of superintendents. Superintendents leading school districts that exceeded the maximum allowable tax levy limit in either or both May 2012 and May 2013 were interviewed about change, school communication, and collaboration with building administrators, faculty and staff, students, parents and community members during the budget development process. A qualitative study was selected to help develop deep understanding about the perceptions of superintendents. The research questions were used to guide the study and gather data to investigate the leadership strategies superintendents implemented in response to changes in school district budget development since the 2011 Real Property Tax Cap legislation. Conclusions drawn from research questions revealed that the superintendents at districts that exceeded the maximum allowable tax levy limit found they needed to alter communication and collaboration practices in response to the Real Property Tax Levy legislation. Communication changes reported by the superintendents were the uses of new communication tools such as automatic phone calling systems, videos and video streaming, additional district newsletters and local televised media coverage. Collaboration changes reported by the superintendents were the use of forums to gather members of the community together to discuss the budget, sharing information with faculty to strengthen understanding, and involving students in various aspects of budget development. The superintendents in this study reaffirmed the value of communication and collaborative leadership functions during budget development when presenting a budget exceeding the maximum allowable tax levy limit.
In this paper, design and fabrication of a commemorative plaque are described and presented. The plaque was fabricated to honour the memory of the 14 women massacred at L＇Ecole Polytechnique in ...Montreal. This plaque is the result of a project partnership between the Faculties of Engineering and Fine Arts, and was sponsored by the Office of the Vice-President Academic and Provost. An art design was selected through a contest coordinated by the Visual Arts Departmment. The selected art design was then turned over to the Mechanical Engineering Department to be converted to a 3-dimensional （3D） solid model and then eventually fabricated on a computer numerical control （CNC） milling machine. The fabricated plaque was unveiled during the December 2010 Memorial event at UVic.
Indiana University-Purdue University Indianapolis (IUPUI)
Previous research on post-conflict elections has found several criteria important in determining if an area is ready to hold elections and ...whether or not it is likely to succeed. Although rarely ranked in any determination of importance, several concepts are present in most post-conflict election research. Additionally, there is not an agreed set of standard criteria upon which success can be assumed. When researching the post-conflict election literature two questions arise: (1) is there a set of criteria established to determine if an area is ready to conduct post-conflict elections, and (2) do all criteria need to be present in order to ensure successful post-conflict elections? Most research agrees on common criteria but highlights or researches one dominant criterion, to which is then often attributed to the success of an election. This is found in Krishna Kumar’s focus on international assistance (Kumar, 1998), Staffan Lindberg’s attribution of success to repetition of the election process (Lindberg, 2006), Paul Collier’s focus on per capita income (Collier, 2009), and Marie-Soleil Frere’s research on post-conflict elections and the media (Frere, 2011). When reviewing multiple research sources, it is likely several factors at various times and in various elections will be credited with being the single source criterion for success. This kind of past research is well supported and conclusively argued, but still fails to provide a scope of understanding outside of a single event. In other words, it is case specific and not comparatively applicable across cases. Although this thesis does not intend to “McDonaldize” (Ritzer, 2009) the process of democratization, it does propose to define a common set of criteria necessary, even if in varying degrees, to conduct successful elections in post-conflict environments.
In this paper we organize research on work-related identities into a four-perspective typology that captures different ways identities can be "positive." Each perspective on positive identity—virtue, ...evaluative, developmental, and structural—highlights a different source of positivity and opens new avenues for theorizing about identity construction. We use these four perspectives to develop propositions about how different forms of positive work-related identity construction can strengthen employees through building social resources.
Statistically model the likelihood of changes in the activities of daily living (ADLs) over time for three groups of older adults: those on a pension at all time periods, those never on a pension, ...and those who transition onto a public pension.
Our study used data from the Canadian Longitudinal Study on Aging (CLSA), a large national survey. We used data from baseline (2010-2015) and the first follow-up wave (2015-2018). We used logistic regression to model the likelihood of ADL changes in males and females by pension receipt status, controlling for several potential confounders and allowing for the impact of public pensions to be modified by baseline income.
The magnitudes of the estimates indicated that those who transition to a public pension are less likely to report ADL degradation and more likely to report ADL improvement compared to those with no public pension. In the lowest baseline income group, those who transitioned onto a pension at follow-up had a 15% (male) or 11% (female) lower likelihood of reporting degraded ADL scores compared to those not receiving a pension at follow-up. Those who transitioned onto a pension in the lowest income group were more likely to report an improved ADL score at follow-up.
Our results could provide evidence for the potential health benefits of more comprehensive guaranteed annual income programs beyond the pension program. The penalty of being low-income was mitigated by the stability of the pension income in terms of ADL improvement or degradation.
Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for ...our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that metabolomic profiles are mainly comprised of fungi derived features, indicating that fungi are the key contributors to small molecules in BFIs. LC-inductively coupled plasma MS (LC-ICP-MS) and MS/MS based dereplication using database searching revealed the presence of several known fungal specialized metabolites and structurally related analogues in these extracts, including siderophores such as desferrichrome, desferricoprogen, and palmitoylcoprogen. Among these analogues, a novel putative coprogen analogue possessing a terminal carboxylic acid motif was identified from
Scopulariopsis
sp. JB370, a common cheese rind fungus, and its structure was elucidated
via
MS/MS fragmentation. Based on these findings, filamentous fungal species appear to be capable of producing multiple siderophores with potentially different biological roles (
i.e.
various affinities for different forms of iron). These findings highlight that fungal species are important contributors to microbiomes
via
their production of abundant specialized metabolites and that elucidating their role in complex communities should continue to be a priority.
Bacterial-fungal interactions (BFIs) were explored in pairwise co-cultures of species from the cheese rind microbiome, revealing that fungi are key contributors to small molecule mediate BFIs and are important contributors to microbiomes.
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